Needing another source of income outside of my art, I planned on working as a coder for pet sites (mysidia powered and no). The problem is I'm only familiar with working with the mys script, which a majority don't use. Would things be that much different? Of course, if they used another framework than I would need to familiarize myself with it, but some don't use frameworks at all and build from the ground up. Would people expect me to know how it works out the box?

Well Mysidia is different from other PHP frameworks, since at this moment it doesnt use a full-fledged framework and everything was built from scratch. If you try using a PHP framework, it will be a bit different. I would still recommend you to do this, since it saves you a huge amount of time from reinventing the wheels.